Microarray technologies have provided many new opportunities for generating genomic-scale datasets, including comprehensive profiles of RNA transcript abundance, and genome-wide analyses of sequence polymorphisms. Taking advantage of the recently completed genome sequence for Toxoplasma gondii , a protozoan parasite responsible for neurological birth defects during congenital infection, and encephalitis in immunosuppresssed patients, we describe the design of a custom multi-functional oligonucleotide microarray. This novel, economical array design supports (i) expression profiling of all annotated genes in the parasite genome, (ii) transcript discovery studies interrogating additional candidate genes, (iii) typing of single nucleotide polymorphisms genome-wide, and (iv) a variety of pilot-scale projects (exon array analysis, antisense expression, organellar genome expression, host immune response profiling, SNP discovery, etc). The expression profiling studies reported here provide the first comprehensive view of the T. gondii transcriptome, yielding insights into key expression programs, such as the developmental switch between the rapidly growing lytic tachyzoites responsible for acute disease, and the latent immune-resistant brady-zoite tissue cysts that reactivate as opportunistic pathogens of immunocompromised individuals. Custom genotyping methods allowed identification of recombination points in the clonal progeny of sexual crosses, providing high-resolution mapping of phenotypic traits such as virulence. These arrays, and the analysis tools developed in the context of this dissertation, are now in widespread use throughout the Toxoplasma research community. Anticipating the imminent availability of a large repository of T. gondii array data, we have also assessed data-intensive automated methods for learning gene regulatory interactions.
